Bibliographic details of the publications referred to by author in this specification are collected at the end of the description.
Reference to any prior art in this specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in Australia or any other country.
The rapidly increasing sophistication of DNA technology is greatly facilitating research and development in a range of disciplines including the medical and allied health industries, the agricultural and horticultural sectors and in the screening of related genomic sequences in environmental samples. Of particular importance is the application of molecular approaches to the characterization of bacterial communities. Such approaches overcome the limitations imposed by culture-mediated techniques for detecting microorganisms. It is known that the unculturable fraction of a microbial population represents a major component of all microbial communities (1, 2, 3).
Culture dependent methods for enumerating bacterial numbers are known to be biased since bacteria can only be cultivated if their metabolic and physiological requirements can be reproduced in vitro. These techniques may take several days to yield a result and, therefore, are inappropriate in situations where rapid diagnostic decisions are required. Where complex fastidious microbial communities are under investigation, such as the variety of microbial habitats in the oral cavity, enumerating bacteria by traditional microbial culturing techniques may also produce erroneous results.
Fluorescence-based methods for detecting bacteria can also be used to enumerate bacteria. For instance, flow cytometry can be applied to the rapid and automated counting of pure cultures used in industrial applications such as the food and biotechnology industries. However, most bacteria are optically too similar to resolve from each other or from debris using flow cytometry, without artificially modifying the target bacteria using fluorescent labelling techniques such as fluorescent antibodies or fluorescent dyes (4). The fluorescent DNA stain, diamidinopheylindole (5), for example, can be used to enumerate complex bacterial populations. However, differences in bacterial cell size, coaggregation of bacteria and the presence of different contaminating matrices (e.g. mud, food, dental plaque, dentine) can make meaningful counting difficult if not problematic as it can with direct or fluorescence microscopy (4).
Rapid enumeration of bacteria can also be achieved using a variety of molecular approaches (1, 2, 3, 6). Generally, however, multiple primers are required to detect the bacteria of interest. Techniques, such as competitive PCR (7, 8), are labour intensive and require the analysis of results from multiple reactions for each test sample. There is a need, therefore, to develop improved molecular approaches to microbial detection and enumeration.
Real-time PCR such as the TaqMan (Registered trade mark) system developed by Applied Biosystems relies on the release and detection of a fluorogenic probe during each round of DNA amplification. It allows for the rapid detection and quantification of DNA without the need for post-PCR processing such as gel electrophoresis and radioactive hybridization (9). In addition, the built-in 96 well format greatly increases the number of samples that can be simultaneously analyzed. The method uses the 5′ exonuclease activity of a Taq polymerase (AmpliTaq Gold, PE Biosystems (Foster City, Calif., USA) during primer extension to cleave a dual-labelled, fluorogenic probe hybridized to the target DNA between the PCR primers. Prior to cleavage, a reporter dye, such as 6-carboxyfluorescein (6-FAM) at the 5′ end of the probe is quenched by 6-carboxy-tetramethylrhodamine (TAMRA) through fluorescent resonance energy transfer. Following digestion, FAM is released. The resulting fluorescence is continuously measured in real-time at 518 nm during the log phase of product accumulation and is proportional to the number of copies of the target sequence.
In work leading up to the present invention, the inventors developed a set of oligonucleotides in the form of primers and probes which universally permit detection and quantification of the total bacterial load within a sample. The primers and probes are directed to 16S rDNA or its 16S rRNA and are conveniently used with real-time PCR or similar or related technology to detect and enumerate any microorganism not being a Eucarya or Archea. The development of a universal primer-probe set permits the rapid and accurate determination of microbial load without necessitating the development of specific primers for particular microorganisms. However, such specific primers may additionally be used to identify microorganisms at the genus or species level. The present invention further provides nucleic and extraction procedures useful inter alia in screening total biota for the presence of microorganisms.